Nothing
R/app_ui.R
In ssd4mosaic: Web Application for the SSD Module of the MOSAIC Platform
Defines functions
golem_add_external_resources
app_ui
#' The application User-Interface
#'
#' @param request Internal parameter for `{shiny}`.
#' DO NOT REMOVE.
#' @import shiny
#' @noRd
app_ui <- function(request) {
tagList(
# Leave this function for adding external resources
golem_add_external_resources(),
shinyjs::useShinyjs(),
shinybusy::add_busy_gif(src = "www/img/wait-animation-tr.gif",
position = "top-right",
height = 117, width = 249,
margins = c(120, 10)),
# Your application UI logic
fluidPage(
div(style = "justify-content: space-between;display: flex;",
div(
a(img(src = "www/img/logo.png", alt = "Logo"),
href = "http://mosaic.univ-lyon1.fr", TARGET="_blank")
),
div(
tags$nav(
tags$ul(id = "navigation_menu",
tags$li(a(
img(src = "www/img/ssd-logo.png", alt = "SSD", class = "logo"),
href = "", TARGET = "_blank") # target to self
),
tags$li(
img(src = "www/img/surv-logo.png", alt = "Survival", class = "logo"),
tags$ul(class = "submenu",
tags$li(a("Standard",
href = "https://mosaic.univ-lyon1.fr/survival",
TARGET = "_blank")),
tags$li(a("GUTS-fit",
href = "https://mosaic.univ-lyon1.fr/guts",
TARGET = "_blank")),
tags$li(a("GUTS-predict",
href = "https://lbbe-shiny.univ-lyon1.fr/guts-predict/",
TARGET = "_blank"))
)
),
tags$li(a(
img(src = "www/img/repro-logo.png", alt = "Reproduction", class = "logo"),
href = "https://mosaic.univ-lyon1.fr/repro", TARGET = "_blank")
),
tags$li(a(
img(src = "www/img/growth-logo.png", alt = "Growth", class = "logo"),
href = "https://mosaic.univ-lyon1.fr/growth", TARGET = "_blank")
),
tags$li(a(
img(src = "www/img/bioacc-logo.png", alt = "Bioaccumulation", class = "logo"),
href = "https://mosaic.univ-lyon1.fr/bioacc", TARGET = "_blank")
),
tags$li(a(
img(src = "www/img/info-logo.png", alt = "Info"),
href = "https://mosaic.univ-lyon1.fr/info", TARGET = "_blank")
),
tags$li(a(
img(src = "www/img/courses-logo.png", alt = "Courses",),
href = "https://mosaic.univ-lyon1.fr/courses", TARGET = "_blank",
div("Courses"))
),
tags$li(a(
img(src = "www/img/team-logo.png", alt = "Team"),
href = "https://mosaic.univ-lyon1.fr/team", TARGET = "_blank",
div("Team"))
),
tags$li(a(
img(src = "www/img/contact-logo.png", alt = "Contact"),
href = "https://mosaic.univ-lyon1.fr/contact", TARGET = "_blank",
div("Contact"))
)
)
))
),
#### Tool presentation ####
div(style = "margin:2em 8% 0",
fluidRow(
column(width = 2, img(src = "www/img/ssd-application-logo.png", alt = "Big logo")),
column(width = 10,
p(tags$b("Species sensitivity distribution"), "(SSD) is an approach to
define safe levels for toxic compounds in an ecosystem. It is based
on the assumption that species sensitivity to a given contaminant can
be described by a probability distribution estimated from toxicity
experiments."),
p("Based on this framework, ",HTML("<b>MOSAIC<sub><i>SSD</i></sub></b>"),
" is able to estimate the so-called ", tags$b("hazardous concentration
for x% of the species"), " (HCx), even when the toxicity values are
censored",
mod_infobutton_ui("infobutton_cens")),
p(HTML("<b>MOSAIC<sub><i>SSD</i></sub></b>")," is based on the ",
a("R", href = "http://www.r-project.org/", TARGET = "_blank"),
" package ",
a("fitdistrplus",
href = "http://cran.r-project.org/web/packages/fitdistrplus/index.html",
TARGET = "_blanl"), ". For more details, please consult the companion ",
a("paper", href = "http://arxiv.org/abs/1311.5772", TARGET = "_blank"),
"."),
actionButton("tutorial", label = "Tutorial",
onclick = "window.open('www/tutorial.html')"),
actionButton("faq", label = "FAQ",
onclick = "window.open('https://mosaic.univ-lyon1.fr/ssd-faq/')",
style = "margin-left:10px;")
)
),
div(id = "tabs_right",
#### Input ####
tabsetPanel(id = "tabs",
tabPanel("Input",
wellPanel( style = "border-top-style: none;",
div(style = "float:right;",
mod_infobutton_ui("infobutton_data"),
tags$label(`for` = "loadFile",
tags$span(class = "btn btn-default btn-file smallButton",
"Load from file")),
tags$input(id = "loadFile", name = "loadFile", type = "file",
style = "position: absolute !important; top: -99999px !important; left: -99999px !important;"),
actionButton("open_example", label = "Try with an example", class = "smallButton"),
actionButton("reset", label = "Reset", class = "smallButton",
onclick = "Shiny.setInputValue('first_plot_done', null);")
),
tags$b("Dataset name: "),
div(class = "inline-input", style = "width: 25em;",
textInput("dataName", label = NULL)),
fluidRow(style = "margin-top: 2em;",
column(width = 7, style = "border-right: 1px solid #333;",
column(width = 7,
rhandsontable::rHandsontableOutput("hot")
),
column(width = 5,
br(),
switchInput("censoredYN", "Censored data", FALSE),
div(tags$b("Censored data"), class = "toggle-text"),
mod_infobutton_ui("infobutton_cens_format"),
br(),
switchInput("col1YN", "Use label 1", FALSE),
div(tags$b("Use label 1"), class = "toggle-text"),
fluidRow(style = "margin-top:-1.75em;",
column(width = 2, offset = 4,
div("As :", style = "display: inline; vertical-align:-0.5em;")
),
column(width = 6,
selectInput("col1Use", label = NULL, choices = c("Names", "Groups"))
)
),
switchInput("col2YN", "Use label 2", FALSE),
div(tags$b("Use label 2"), class = "toggle-text"),
fluidRow(style = "margin-top:-1.75em;",
column(width = 2, offset = 4,
div("As :", style = "display: inline; vertical-align:-0.5em;")
),
column(width = 6,
selectInput("col2Use", label = NULL, choices = c("Names", "Groups"))
)
)
)
),
column(width = 4,
tags$b("Concentration unit"),
div(class = "inline-input", style = "width: 10em; vertical-align: -0.9em;",
selectInput("conc", NULL,
choices = c("Arbitrary unit",
"\u03bcg/L",
"\u03bcmol/L",
"mg/L",
"pg/L",
"ng/L",
"g/L",
"mS/cm\u00b2",
"g/ha"),
selected = "\u03bcg/L")),
br(),
tags$b("Show distributions"),
mod_infobutton_ui("infobutton_dist"),
div(class = "inline-input",
checkboxGroupInput("logDist", label = NULL, choices = c("log-normal" = "lnorm", "log-logistic" = "llogis"), selected = "lnorm", inline = T)
)
)
),
actionButton("run", "Run", icon = icon("rocket"),
style="font-size:150%; float: right; margin-top: -2.5em;",
onclick = "Shiny.setInputValue('first_plot_done', null);")
)),
#### Output ####
tabPanel("Results",
wellPanel( style = "border-top-style: none;",
h2(
div(style = "display: inline;font-family: Comfortaa Regular; color: #ee7202;", "Results"),
"for dataset:", tags$i(textOutput("dataNameDisp", inline = T))),
fluidRow(style="display:flex;", class = "full-height",
column(width = 3,
wellPanel(style = "border-color: #ccc;",
checkboxGroupInput("distDisp", label = "Displayed distributions", choices = c("log-normal" = 1, "log-logistic" = 2), selected = c(1,2)),
switchInput("logscale", "Change x axis scale", TRUE),
div("Log scale on x axis", class = "toggle-text"),
br(),
switchInput("ciDispYN", "Display CI", TRUE),
div("Confidence interval(s)", class = "toggle-text"),
br(),
div(style = "margin-top: -1.2em; margin-left: 67px; margin-bottom: 0px;",
radioButtons("CIlevel", label = NULL,
choices = c("95% CI" = 0.95, "90% CI" = 0.9),
selected = 0.95, inline = TRUE),
mod_infobutton_ui("infobutton_CIlevel_plot")),
switchInput("namesDispYN", "Display names", FALSE),
div("Species Names", class = "toggle-text"),
br(),
switchInput("groupsDispYN", "Display groups", FALSE),
div("Group labels", class = "toggle-text"),
)
),
column(width = 6,
wellPanel(style = "background-color: #fff;",
plotOutput("p", height = "auto")
)
),
column(width = 3,
mod_infobutton_ui("infobutton_CIlevel_values"),
tabsetPanel(
tabPanel(title = "Parameters",
wellPanel(style = "background-color: #fff;",
h4("Parameters values:", style = "display:inline;"),
mod_infobutton_ui("infobutton_param_values"),
br(),
htmlOutput("parameters")
)
),
tabPanel(title = "HCx",
wellPanel(style = "background-color: #fff;",
h4("Estimation of the hazardous concentrations"),
wellPanel(style = "justify-content: center;",
# may need further centering with real values table
tableOutput("HCx")
),
numericInput("customHCx", label = "Get custom HCx", value = 1,
min = 0, max = 100),
verbatimTextOutput("customHCx_output")
)
)
),
wellPanel( style = "height: auto;",
h4("Download report"),
fluidRow(
column(width = 5,
radioButtons("reportFormat", label = NULL, choices = c("pdf", "html", "md"), selected = "pdf")
),
column(width = 7,
downloadButton("report", label = "Download", class = "smallButton", style = "margin-top: 1.5em;")
)
)
)
)
),
h3("R script"),
verbatimTextOutput("codeR", placeholder = T)
)
)
)),
wellPanel(style = "background-color: #fff;",
h1(tags$b("Staff and contributors"), style = "font-size: large;"),
"Elise Billoir, Universit\u00e9 de Lorraine", br(),
"Sandrine Charles, Laboratory of Biometry and Evolutionary Biology", br(),
"Marie Laure Delignette-Muller, VetAgro Sup", br(),
"Mil\u00e9na Kaag, Laboratory of Biometry and Evolutionary Biology", br(),
"Guillaume Kon Kam King, French National Research Institute for Agriculture, Food and the Environment", br(),
"Philippe Veber, Laboratory of Biometry and Evolutionary Biology"
)
)
)
)
}
#' Add external Resources to the Application
#'
#' This function is internally used to add external
#' resources inside the Shiny application.
#'
#' @import shiny
#' @importFrom golem add_resource_path activate_js favicon bundle_resources
#' @noRd
golem_add_external_resources <- function() {
add_resource_path(
"www",
app_sys("app/www")
)
tags$head(
favicon(),
bundle_resources(
path = app_sys("app/www"),
app_title = "MOSAIC SSD"
)
# Add here other external resources
# for example, you can add shinyalert::useShinyalert()
)
}
Try the ssd4mosaic package in your browser
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ssd4mosaic documentation built on April 4, 2025, 1:42 a.m.
R Package Documentation
Browse R Packages
We want your feedback!
Note that we can't provide technical support on individual packages. You should contact the package authors for that.
Defines functions golem_add_external_resources app_ui
#' The application User-Interface
#'
#' @param request Internal parameter for `{shiny}`.
#' DO NOT REMOVE.
#' @import shiny
#' @noRd
app_ui <- function(request) {
tagList(
# Leave this function for adding external resources
golem_add_external_resources(),
shinyjs::useShinyjs(),
shinybusy::add_busy_gif(src = "www/img/wait-animation-tr.gif",
position = "top-right",
height = 117, width = 249,
margins = c(120, 10)),
# Your application UI logic
fluidPage(
div(style = "justify-content: space-between;display: flex;",
div(
a(img(src = "www/img/logo.png", alt = "Logo"),
href = "http://mosaic.univ-lyon1.fr", TARGET="_blank")
),
div(
tags$nav(
tags$ul(id = "navigation_menu",
tags$li(a(
img(src = "www/img/ssd-logo.png", alt = "SSD", class = "logo"),
href = "", TARGET = "_blank") # target to self
),
tags$li(
img(src = "www/img/surv-logo.png", alt = "Survival", class = "logo"),
tags$ul(class = "submenu",
tags$li(a("Standard",
href = "https://mosaic.univ-lyon1.fr/survival",
TARGET = "_blank")),
tags$li(a("GUTS-fit",
href = "https://mosaic.univ-lyon1.fr/guts",
TARGET = "_blank")),
tags$li(a("GUTS-predict",
href = "https://lbbe-shiny.univ-lyon1.fr/guts-predict/",
TARGET = "_blank"))
)
),
tags$li(a(
img(src = "www/img/repro-logo.png", alt = "Reproduction", class = "logo"),
href = "https://mosaic.univ-lyon1.fr/repro", TARGET = "_blank")
),
tags$li(a(
img(src = "www/img/growth-logo.png", alt = "Growth", class = "logo"),
href = "https://mosaic.univ-lyon1.fr/growth", TARGET = "_blank")
),
tags$li(a(
img(src = "www/img/bioacc-logo.png", alt = "Bioaccumulation", class = "logo"),
href = "https://mosaic.univ-lyon1.fr/bioacc", TARGET = "_blank")
),
tags$li(a(
img(src = "www/img/info-logo.png", alt = "Info"),
href = "https://mosaic.univ-lyon1.fr/info", TARGET = "_blank")
),
tags$li(a(
img(src = "www/img/courses-logo.png", alt = "Courses",),
href = "https://mosaic.univ-lyon1.fr/courses", TARGET = "_blank",
div("Courses"))
),
tags$li(a(
img(src = "www/img/team-logo.png", alt = "Team"),
href = "https://mosaic.univ-lyon1.fr/team", TARGET = "_blank",
div("Team"))
),
tags$li(a(
img(src = "www/img/contact-logo.png", alt = "Contact"),
href = "https://mosaic.univ-lyon1.fr/contact", TARGET = "_blank",
div("Contact"))
)
)
))
),
#### Tool presentation ####
div(style = "margin:2em 8% 0",
fluidRow(
column(width = 2, img(src = "www/img/ssd-application-logo.png", alt = "Big logo")),
column(width = 10,
p(tags$b("Species sensitivity distribution"), "(SSD) is an approach to
define safe levels for toxic compounds in an ecosystem. It is based
on the assumption that species sensitivity to a given contaminant can
be described by a probability distribution estimated from toxicity
experiments."),
p("Based on this framework, ",HTML("<b>MOSAIC<sub><i>SSD</i></sub></b>"),
" is able to estimate the so-called ", tags$b("hazardous concentration
for x% of the species"), " (HCx), even when the toxicity values are
censored",
mod_infobutton_ui("infobutton_cens")),
p(HTML("<b>MOSAIC<sub><i>SSD</i></sub></b>")," is based on the ",
a("R", href = "http://www.r-project.org/", TARGET = "_blank"),
" package ",
a("fitdistrplus",
href = "http://cran.r-project.org/web/packages/fitdistrplus/index.html",
TARGET = "_blanl"), ". For more details, please consult the companion ",
a("paper", href = "http://arxiv.org/abs/1311.5772", TARGET = "_blank"),
"."),
actionButton("tutorial", label = "Tutorial",
onclick = "window.open('www/tutorial.html')"),
actionButton("faq", label = "FAQ",
onclick = "window.open('https://mosaic.univ-lyon1.fr/ssd-faq/')",
style = "margin-left:10px;")
)
),
div(id = "tabs_right",
#### Input ####
tabsetPanel(id = "tabs",
tabPanel("Input",
wellPanel( style = "border-top-style: none;",
div(style = "float:right;",
mod_infobutton_ui("infobutton_data"),
tags$label(`for` = "loadFile",
tags$span(class = "btn btn-default btn-file smallButton",
"Load from file")),
tags$input(id = "loadFile", name = "loadFile", type = "file",
style = "position: absolute !important; top: -99999px !important; left: -99999px !important;"),
actionButton("open_example", label = "Try with an example", class = "smallButton"),
actionButton("reset", label = "Reset", class = "smallButton",
onclick = "Shiny.setInputValue('first_plot_done', null);")
),
tags$b("Dataset name: "),
div(class = "inline-input", style = "width: 25em;",
textInput("dataName", label = NULL)),
fluidRow(style = "margin-top: 2em;",
column(width = 7, style = "border-right: 1px solid #333;",
column(width = 7,
rhandsontable::rHandsontableOutput("hot")
),
column(width = 5,
br(),
switchInput("censoredYN", "Censored data", FALSE),
div(tags$b("Censored data"), class = "toggle-text"),
mod_infobutton_ui("infobutton_cens_format"),
br(),
switchInput("col1YN", "Use label 1", FALSE),
div(tags$b("Use label 1"), class = "toggle-text"),
fluidRow(style = "margin-top:-1.75em;",
column(width = 2, offset = 4,
div("As :", style = "display: inline; vertical-align:-0.5em;")
),
column(width = 6,
selectInput("col1Use", label = NULL, choices = c("Names", "Groups"))
)
),
switchInput("col2YN", "Use label 2", FALSE),
div(tags$b("Use label 2"), class = "toggle-text"),
fluidRow(style = "margin-top:-1.75em;",
column(width = 2, offset = 4,
div("As :", style = "display: inline; vertical-align:-0.5em;")
),
column(width = 6,
selectInput("col2Use", label = NULL, choices = c("Names", "Groups"))
)
)
)
),
column(width = 4,
tags$b("Concentration unit"),
div(class = "inline-input", style = "width: 10em; vertical-align: -0.9em;",
selectInput("conc", NULL,
choices = c("Arbitrary unit",
"\u03bcg/L",
"\u03bcmol/L",
"mg/L",
"pg/L",
"ng/L",
"g/L",
"mS/cm\u00b2",
"g/ha"),
selected = "\u03bcg/L")),
br(),
tags$b("Show distributions"),
mod_infobutton_ui("infobutton_dist"),
div(class = "inline-input",
checkboxGroupInput("logDist", label = NULL, choices = c("log-normal" = "lnorm", "log-logistic" = "llogis"), selected = "lnorm", inline = T)
)
)
),
actionButton("run", "Run", icon = icon("rocket"),
style="font-size:150%; float: right; margin-top: -2.5em;",
onclick = "Shiny.setInputValue('first_plot_done', null);")
)),
#### Output ####
tabPanel("Results",
wellPanel( style = "border-top-style: none;",
h2(
div(style = "display: inline;font-family: Comfortaa Regular; color: #ee7202;", "Results"),
"for dataset:", tags$i(textOutput("dataNameDisp", inline = T))),
fluidRow(style="display:flex;", class = "full-height",
column(width = 3,
wellPanel(style = "border-color: #ccc;",
checkboxGroupInput("distDisp", label = "Displayed distributions", choices = c("log-normal" = 1, "log-logistic" = 2), selected = c(1,2)),
switchInput("logscale", "Change x axis scale", TRUE),
div("Log scale on x axis", class = "toggle-text"),
br(),
switchInput("ciDispYN", "Display CI", TRUE),
div("Confidence interval(s)", class = "toggle-text"),
br(),
div(style = "margin-top: -1.2em; margin-left: 67px; margin-bottom: 0px;",
radioButtons("CIlevel", label = NULL,
choices = c("95% CI" = 0.95, "90% CI" = 0.9),
selected = 0.95, inline = TRUE),
mod_infobutton_ui("infobutton_CIlevel_plot")),
switchInput("namesDispYN", "Display names", FALSE),
div("Species Names", class = "toggle-text"),
br(),
switchInput("groupsDispYN", "Display groups", FALSE),
div("Group labels", class = "toggle-text"),
)
),
column(width = 6,
wellPanel(style = "background-color: #fff;",
plotOutput("p", height = "auto")
)
),
column(width = 3,
mod_infobutton_ui("infobutton_CIlevel_values"),
tabsetPanel(
tabPanel(title = "Parameters",
wellPanel(style = "background-color: #fff;",
h4("Parameters values:", style = "display:inline;"),
mod_infobutton_ui("infobutton_param_values"),
br(),
htmlOutput("parameters")
)
),
tabPanel(title = "HCx",
wellPanel(style = "background-color: #fff;",
h4("Estimation of the hazardous concentrations"),
wellPanel(style = "justify-content: center;",
# may need further centering with real values table
tableOutput("HCx")
),
numericInput("customHCx", label = "Get custom HCx", value = 1,
min = 0, max = 100),
verbatimTextOutput("customHCx_output")
)
)
),
wellPanel( style = "height: auto;",
h4("Download report"),
fluidRow(
column(width = 5,
radioButtons("reportFormat", label = NULL, choices = c("pdf", "html", "md"), selected = "pdf")
),
column(width = 7,
downloadButton("report", label = "Download", class = "smallButton", style = "margin-top: 1.5em;")
)
)
)
)
),
h3("R script"),
verbatimTextOutput("codeR", placeholder = T)
)
)
)),
wellPanel(style = "background-color: #fff;",
h1(tags$b("Staff and contributors"), style = "font-size: large;"),
"Elise Billoir, Universit\u00e9 de Lorraine", br(),
"Sandrine Charles, Laboratory of Biometry and Evolutionary Biology", br(),
"Marie Laure Delignette-Muller, VetAgro Sup", br(),
"Mil\u00e9na Kaag, Laboratory of Biometry and Evolutionary Biology", br(),
"Guillaume Kon Kam King, French National Research Institute for Agriculture, Food and the Environment", br(),
"Philippe Veber, Laboratory of Biometry and Evolutionary Biology"
)
)
)
)
}
#' Add external Resources to the Application
#'
#' This function is internally used to add external
#' resources inside the Shiny application.
#'
#' @import shiny
#' @importFrom golem add_resource_path activate_js favicon bundle_resources
#' @noRd
golem_add_external_resources <- function() {
add_resource_path(
"www",
app_sys("app/www")
)
tags$head(
favicon(),
bundle_resources(
path = app_sys("app/www"),
app_title = "MOSAIC SSD"
)
# Add here other external resources
# for example, you can add shinyalert::useShinyalert()
)
}
Try the ssd4mosaic package in your browser
Any scripts or data that you put into this service are public.
R Package Documentation
Browse R Packages
We want your feedback!
Note that we can't provide technical support on individual packages. You should contact the package authors for that.
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